PMD: Total War
by runesage86
Summary: What would have happened if Humans and Pokemon hadn't gotten along when they first met? What if the Poke Ball had never been invented? Unfortunately for everyone involved, they went to war, with Humans developing technology to counteract the Pokemon's vastly superior abilities. Now it seems like there is no sign of it stopping. In the midst of this, a human wakes up as a Pokemon...
1. Chapter 0

Chapter 0: The Sacrifice.

A form clad in white dashed through the facility, navigating the dark tunnels with ease. Footsteps rang through the halls along with shouts, but the figure didn't take much notice of them. They were on a mission. A mission that could… There! A set of small objects on the table caught the figure's attention. He hurriedly searched through the clutter, and muttered, "Come on. I know that they're all here. I counted them myself." He set three aside and frantically searched more for the fourth one. "Got you!" The figure held the four objects in his hand. "O guardian of doorways, please hear my plea. Save me from danger and grant me an audience!" The four objects in the figure's hand flashed, and a circular opening in space appeared before them.

"Stop him!" The pursuers shouted, but it was too late. The figure stepped through the doorway, and it vanished. "What are we going to tell the Boss?" The voice asked. "We failed."

"'e can't do much. No one who steps through that doorway lives. We report a success." A second voice replied. "Come on. We need to make it look like we weren't here. Make sure that you leave…" the second voice faded off into the distance.

…

The figure opened his eyes to see a rather curious sight. All around him, rings floated in the air, with images in the middle of them. A rather small figure was watching through one of the rings. "You requested an audience with me?" The figure said.

"Y-y-yes. I suppose I did." The white-clad figure said. "I need some help."

"That's what I'm here for!" The small figure said gleefully. "I am Hoopa, the ruler of doorways, and one of two granters of wishes. I love making bargains. Come, let us discuss terms. What is it that you want done?"

"I want this war to end, without one side killing the other."

A silence followed this statement that seemed to stretch on into infinity. "I can't change people or Pokemon's minds." Hoopa said. There was a pleased gleam in his eye, that indicated that this was something he'd been desiring for a long time.

"I'm not asking for it to be done now. I just want it to happen. I don't care how long it takes. I just need to know that the senseless violence will end with peace between the two." The figure looked hopeful. "Surely you could set some events in motion that would cause that."

Hoopa considered, weighing the options and the scope of his abilities. "This is a huge wish. I cannot do it on my own. It will take me and Jirachi working together to set the events in motion, and even then, I cannot guarantee that it will end the way you want. However, the way things are currently going, there is no chance that the war will end with both sides intact."

"I'm willing to take that risk. Too much has been lost because of this war for me to stand by and watch." The white clad figure announced.

"Except you haven't been 'just watching' have you?" Hoopa played absentmindedly with the ring on his left ear. The white clad figure flushed slightly, remembering who he was speaking to. Seeming to come to a decision, Hoopa removed the ring and tossed it into the air, where it expanded slightly. "Jirachi. You awake, or do I need to come get you?"

Another small figure sleepily poked her head out of the ring. "No need to be rude. You wanted…" Jirachi yawned expressively, "me, Hoopa?"

"This one wishes for a peaceful end to the war." Hoopa replied.

It seemed to take several seconds for the words to pierce the sleepiness of Jirachi, but once they did, her eyes opened wide. "Finally, someone asked for that. It will not be easy, for anyone involved. Especially you." Jirachi looked at the figure standing before the two legends.

"I am willing to pay any price needed."

"But are you _really_? Normally we would test your will before granting the wish. However, since Hoopa and I have both wanted this for a long time, this one's going to be a little different." Jirachi and Hoopa looked at each other for a second. "You will be dead to all those who knew you, yet still live. Unknown to those around you, and unable to communicate with those you love. Some of your memories will be claimed as well, to prevent you from seeking them out. Yet, you will also serve a great purpose. You will have the power to sense the path that leads to peace, and will be able to appear when things are not going down that path." Jirachi's eyes softened. "This is simultaneously the fulfillment of your wish and the price. You will have the sense of foresight, and the responsibility to act on it. You will save many lives with your abilities, yet you will seldom be appreciated. We will set in motion everything we can do, but the rest will be up to you, and several others. Do you understand what will happen?"

The figure seemed taken aback. "I thought- no. It couldn't be that easy, could it."

"Few things are. If you'd asked for something that'd only affect yourself, it would be easier for us and you. The more people a wish affects, the more energy it takes, on everyone's part." Jirachi said.

"I understand, and I accept." The figure said.

"Then the pact is sealed." Hoopa stated. "I hope you succeed, for the world's sake." His form began to shift, and suddenly a much larger being stood in front of the figure. Jirachi's chest fluttered and a third eye appeared, which immediately began to glow. The giant Hoopa began chanting something in a mystical language, and several of the objects which the figure had used to enter this realm began to appear, swirling around him. The symbols on the objects peeled off, and began spinning faster and faster, while Jirachi's eye glowed more and more. The figure began wondering if he was making the right choice. _Too late for that now I guess. Let's see where this takes me._ A beam of light shot from Jirachi's chest and slammed into the white clad figure at the same time as the swirling symbols shot from their orbit around Hoopa and into the figure as well.

The last thing the figure knew before he blacked out was pain. Intense pain.


	2. Chapter 1

Chapter 1: Waking up

Sil woke up to silence. This confused him, because it was never quiet in his house. There was always somebody coming and going, and it was always about the war. He reached up to push his blanket off of him, and nearly scratched himself through the thick mat of fur that was now covering his body. There were about two seconds where his sleepy brain processed that information, and then his eyes shot open. He sat up thoroughly confused, and scanned his body. _What the… I'm…_ His thought process trailed off as he stared at his fur coated hands, no, _paws_. _I'm some kind of monster._ His thoughts were surprisingly calm for the events that were currently occurring. _Funny, I was human yesterday._ He was taking this rather well, until the next realization came in.

 _I'm gonna be hunted now. I'm the enemy._ Sil's breathing sped up, his heart began to race. Looking around, he took stock of his surroundings. _Where am I? If I know where I am… I should be able to tell how much danger I'm in._ He looked around at the trees surrounding him. _I can't… I'm too short!_ There was no way for him to tell where he was. The trees towered above him. If he had to guess, he'd say he was only two feet tall. As he looked around, still trying desperately to make sense of what had happened, he noticed an object at his feet. _That's… my backpack? No, that's not possible, but… it's just as torn as mine was, and it has that faded spot. It's so much smaller than it should be…_ He thought about it for a few seconds, then, since nothing was making sense anyway, shrugged, and attempted to put it on, staggering slightly as it weighed more than he thought. _That, or I'm just weaker._

Sil peered into the bag. Inside, it contained some apples, some other fruits, and a few bottles of some kind of drink. _What are all these…_ The day just kept on getting weirder and weirder. Something inside him, however, told him that he would need these. _Food is always nice, I guess._ He thought, trying to puzzle the feeling out. He looked around him again, trying to collect his bearings one last time, before giving up and moving out of the clearing.

Sil continued through the forest, still trying to recognize something, _anything,_ that would give him a clue as to where he was, yet nothing jumped out at him as being familiar. _Wait, why am I trying to find out where I am? I'm terrible with directions on a normal day, much less a day that's as strange as this._ Strangely, this realization comforted him. If he didn't know any way was the wrong way, then every way must be the right way. A slight smile crossed his face and he set off in no particular direction. As Sil continued along, humming a tune to himself, a gunshot rang out in the distance. Immediately Sil ducked for cover. _Where was that? It came from over there. Monsters don't have guns, so they must be human. Hunters._ Suddenly little things he hadn't realized he'd been noticing came together and he realized, _very_ generally, where he was. _Oh Arceus. I'm in 23's area. I'm dead._ Base 23 was known for their ruthlessness at targeting any monsters and eliminating them. It had gotten so crazy that, behind their backs, other bases referred to them as the Loose Cannons. Sil's mind went into full panic mode. _I'm dead. I'm so dead._

"Hello there!" A voice came from right behind Sil.

Immediately, Sil spun around. _"BACK OFF!"_ An instinctual reaction made his ears fly open, and a immense wave of force flew out from him, knocking the intruder into a tree. The figure collapsed to the ground, completely stunned. A second or two passed without the intruder stirrings, and, after calming down slightly, Sil crept closer to the figure, not knowing whether or not to hope it was knocked out or not. It was a small, mouse-like creature with red ears, and a red plus shaped tail, and somehow Sil knew he was male. As Sil examined the strange creature, a motion on his right caught his eye. Shadowy tendrils snaked their way across the ground from a new assailant, and before Sil could react, they bound him in a dark cage.

"Give me one good reason why I shouldn't kill you now." The assailant said, black electricity sparking across their body. She—once again, Sil could inexplicably tell—looked almost the same as the downed figure except with blue ears and a blue minus shaped tail.

Sil tried to talk, but for some reason his voice wouldn't work very well. "Urrr…" A groan made its way past his lips, but he wasn't used to the way his mouth tried to shape the words. Thoughts began racing in his mind. _What did I do? Was he her friend? Oh… Why did I have to do that? I didn't even know what I'm doing._ Another thought came to him. _"If she doesn't kill me, the Loose Cannons will."_

A very strange expression crossed the face of his assailant. "Loose Cannons? How do you know 23's nickname?"

 _Wait did she hear my THOUGHTS!?_ Sil was really beginning to panic now, trying desperately to activate that force wave again, and failing miserably, then what she said clicked. He tried forming words with his mouth again, but could not make the words form. He tried a different approach. _"Wait you were a human too?"_ He thought, trying to make them as… well… audible as possible.

The figure sighed, then waved her hand dismissively. "Wake up Lyle. We've got to get out of here." She, not too gently, kicked the resting figure.

"Oh come on Mina. I was just slammed into a tree. The least you could do is let me rest for a while." Lyle said, his eyes still closed on the ground in a resting position. "Sorry about sneaking up on you there, bud. We're just in dangerous territory."

"He knows, and that's why there's no time for your shenanigans." Mina said, keeping a wary eye on their surroundings.

"Oh fine..." Lyle said, getting up and dusting himself off. "So, you've got some type of psychic abilities. Telepathy and telekinesis. You have any other abilities?" Lyle asked turning to Sil.

 _Telepathy, huh? That means I'm projecting my thoughts, right? In that case…_ Sil thought to himself. _"Umm… I don't know…"_ he replied. _"I'm not used to this… Honestly I'm kind of hoping you guys can help me figure that out."_

"Hmm… could be an interesting puzzle to figure out… You're some kind of psychic type, that's for sure, but I don't think I've seen any of your kind before…" Lyle's eyes seemed to gleam with excitement about this new puzzle to solve.

"Lyle, now is not the time." Mina said. "Get your magic cards out and get us out of here."

"Ok, first off, they're not _magic_. They're entercards. They tap into ley lines to open up a gate and-"

"Magic." Mina said, cutting off Lyle's explanation. "Now, can we leave now or not?"

"We're not on a line right now, so no." Lyle replied, his hand in a strange pouch he held from over his shoulder. "The nearest one should be in that direction." He pointed through the trees.

"Let's get out of here then." Mina responded, and immediately began heading off, not looking back.

Sil was completely lost at this point. Between what had happened to him earlier today and the exchange between Lyle and Mina, he was more confused than he thought he'd ever be. Lyle beckoned for him to follow, and so he did, trying to make sense out of _anything_ that had happened so far today.

Mina led the group through the underbrush, making sure to leave almost no indication that they were there. The group traveled in silence for a while, keeping alert for anything signaling the presence of Hunters. As the group traveled, a sudden pain flared through Sil's right eye, and he grunted slightly in discomfort. Mina turned around and glared at him, but the glare turned quickly to shock. Sil had little time to take that in, however, as his vision swirled and distorted. He saw two humans outfitted in full hunter gear traveling. The sight continued and he saw one signal to the other, and both raise their guns. Sil's vision followed their gaze and he saw himself, with one eye emitting a strange rainbow halo, Mina, and Lyle.

 _"NO!"_ The mental shout rang from Sil's mind and he raised his hands in another instinct. A green barrier formed around them as two gunshots rang out. The bullets impacted the barrier and disappeared without a trace. The barrier faded, and another shot rang out, impacting Sil's shoulder, sending him staggering. The pain didn't register for a second, then agony shot up his arm. He fell to one knee, an unearthly sound coming from his throat.

"Let's move it! Lyle, I swear if you don't get us out of here right now…" Mina said, pulling Sil through the underbrush.

"I'm working on it!" Lyle had his hands scrambling through a the small pouch. "The ley line should be right there." He pointed at a small opening in the trees.

"Well then get going!" Mina said.

Sil's heart was pounding in his chest. He both knew, and didn't know what was going on. He knew they were about to die, but he didn't know how he'd seen those Hunters, or how he'd formed that barrier. Come to think of it, how did he throw Lyle into that tree earlier? All of these thoughts raced through his mind at breakneck speed, the terror and pain making his brain jump from question to question without a second's break in between. _At least today can't get any weirder,_ he thought to himself.

In his hyper aware, yet strangely distant state, he noticed Lyle pull four small objects out of his bag and link them together into a square shape. He then expertly threw them into the clearing, where they began to glow. A bright pillar of light filled the small clearing, and Lyle, without a second's hesitation, jumped into the light. Before Sil had a chance to think anything beyond, _never mind…_ , Mina dragged him into the pillar.


	3. Chapter 2

The light blinded Sil completely, and he had that strange feeling that comes when you stand up too fast, making him completely dizzy and disoriented. When his mind finally righted himself, he found himself in a strange cavern. However, once the dizziness left him, the pain returned. "Aargh…." Sil managed to groan, clutching his arm tightly.

"Oh right, you got shot." Lyle said, approaching Sil and examining the wound. "Hmm…. You don't happen to have any Oran berries, would you?"

" _I… don't know."_ Sil managed to project. _"There's some stuff in my bag, you can check in there."_ The pain was really beginning to get to him.

Lyle rummaged through the bag, and his eyes widened. "You've got some pretty great stuff in here. Oran berries, some Apples, a few Max Elixers, even some useful seeds." He pulled out a decently sized blue berry, and handed it to Sil. "This will help dull the pain and give you some energy. I'd help you do more, but we can't stay here for long."

" _Why not?"_ Sil asked, eating the berry. It didn't taste particularly good, but he could feel the throbbing pain in his arm recede. He stood up, wincing slightly.

Lyle beckoned for him to follow. "This is what's known as a mystery dungeon. It's an escape for the desperate. We're currently traveling through a ley line." He noticed the blank look on Sil's face and sighed. "Natural lines of energy. Those cards that I threw into the clearing open up a small hole in the ley line, letting us get into it. While this does let us travel across the world pretty quickly, it also has it's risks. We're currently surrounded by massive amounts of energy. It tends to… aggravate those that are in it. The energy builds up around you, trying to assimilate you into the line fully. There are only two ways out of a line. Getting completely knocked out, or creating a warp tile. The further we travel within the dungeon, the further away we'll be from where we entered when we use the warp tile."

" _That doesn't sound too bad. We just have to get as far as we want as fast as we can, right?"_ Sil asked.

"Yes, but there are others in this dungeon who haven't made it out yet. The ley line is beginning to assimilate their bodies, and so they're very desperate. As we go through the dungeon, we have to be careful. Their minds are almost completely focused on getting out, and so they will attack whatever they see." Lyle continued with his explanation.

" _So… we avoid others?"_ Sil asked, confused.

"I like to knock them out. Their energy comes alongside us, and when we exit, they will as well." Lyle said, walking on.

" _Wouldn't they get mad?"_ Sil asked, confused. _"After all, the last thing they would remember would be you knocking them out."_

Lyle laughed. "Not at all. Most of them are actually grateful. Being trapped here is… not pleasant… to say the least." Lyle's face darkened slightly, as if dwelling on an unpleasant memory.

Sil took that as his que to stop asking questions about the dungeon. Looking around at the surroundings, he could feel the immense energy running through the place. It was like a high pitched noise that grated on his consciousness, and he understood how, after enough time, people could become desperate. _"Well, we better get a move on then._ " Sil looked around. _"Where's Mina?"_

Lyle chuckled again. "She's probably already through the dungeon by now. She has a set of Escape Cards, so she should be able to get out when the dungeon ends. I set the endpoint of our travels with the Entercards to be our house, and so she'll know when she can use the cards to leave. Shadows like Mina tend to lose control faster in these dungeons. Their energy becomes especially volatile, and the enter something called Hyper Mode. It actually hurts her to be here, so I don't blame her for leaving as fast as possible." Lyle rubbed the back of his head slightly. "That being said, it's not fun being here for me either, so let's get going."

Sil nodded, and followed Lyle through the twisting hallways of the dungeon. _"Umm… you said you knocked the others out. How do you do that?_ " Sil asked, very concerned about his abilities to keep himself safe.

Lyle looked over at Sil, confused. "You mean you don't know how you used Psychic to throw me into a tree, and Protect to keep us safe from the Hunters?" Sil shook his head, and Lyle shrugged. "I mean, you could just bash whatever's in the way with your fists, but there's better ways for those like you and me to do it." His cheek pouches began to spark, and suddenly a bolt of electrical energy shot out of him to a creature that Sil hadn't noticed. "Most of us have an organ or two that stores their elemental energy. I can focus mine into a burst like that, known as a Discharge, or I can stimulate my muscles to let me go faster. Plus I have a few more tricks up my sleeve for when things go real south. My tail helps gather the energy, and I store it in these cheek pouches." Lyle indicated the two red dots on his face with the plus signs on them. "You're just going to have to find where your energy comes from. If I had to guess…" Lyle looked Sil up and down. "It's probably stored in your eyes, or maybe your ears. I remember seeing your eyes glow right before the Hunters attacked, and when you threw me into the tree, I remember your ears opening wide."

Immediately Sil began to open his ears, and Lyle waved his hands in panic. "Nonononono, don't do it at me! I don't want to get knocked out again." Sil clamped his ears tightly shut. "Just let me handle the fighting for now. We can work on you fighting after we get out of this place." Sil nodded, not even daring to speak in case the ability went out of hand and knocked Lyle out.

They continued through the dungeon, meeting few other creatures. Apparently, this ley line was one that wasn't traveled often, and was usually only for the very desperate. As such, the journey didn't take long until they reached a point they could not pass. An immensely powerful barrier stood between them and the rest of the line, and Lyle began rummaging through his pouch of Entercards. "Here we go…" Lyle connected four cards and threw them on the ground, where they formed a strange tile. "Step on it quickly. It won't last for long." Lyle said, before following his own advice. Not wanting to be left behind, Sil quickly stood on the tile. One more strange dizzy sensation later, and he was standing in another clearing, similar to the one they had fled from. Lyle stood their, talking to a few creatures that Sil recognized from their time in the dungeon. Some of them tried to give Lyle some items, but he shook his head, and waved them off.

After all the creatures had left, Sil saw Mina walk up to Lyle. "You know, we could have used those supplies." Mina said to Lyle.

"It was probably all they had on them. I wanted them to get home safely." Lyle responded. He turned over to Sil just in time to see Sil stagger and fall to his knees, clutching his arm again. "Oh right!" Lyle rushed over and looked over the wound, which had begun bleeding again. "Looks like the Oran effect has worn off… better get that bandaged up."

" _So… hungry…"_ Sil managed to project before another wave of dizziness washed over him. He felt Lyle help him to his feet, and lead him inside a house Sil had not noticed was there, and then gently lay down on a bed. A fruit was placed in his left arm, and Sil managed to take a bite. It was an Apple. Nothing crazy extraordinary, but eating even that single bite managed to quell some of the dizziness. He heard Lyle arguing with Mina, but couldn't make out the words as he finished his apple and sleep overcame him. Hazy dreams floated through his mind; much shouting, screams, a large explosion. Sadness everywhere. Then, a kind face. Not a monster's face, a human's. The human's face took on an expression of sadness, and faded from view. Sil tried to reach out, to stop the human from leaving, to comfort him, but it was too late. The vision shifted to a standoff between humans and monsters, and he was there in the middle, targeted by both sides. A strange white flash darted through his vision, scooping him up as both the humans and the monsters attacked the spot where he'd been. He saw a fox-like face, as well as a blue otter with strange shells. He saw groups of Hunters, angrily chanting with guns raised high, he saw groups of Monsters, energy bursting for them as they prepared for war. Fear for life, an all-encompassing rage, and the faintest of all hopes disappearing into nothing. Sil woke up, gasping for breath, noticing a strange light coming from his right eye that faded into nothing. The dream cycled through his mind, making getting to sleep again difficult, but eventually consciousness faded and he managed to rest for the night.

* * *

Hey this is Runesage here. This has already gotten a few more views than I ever thought it would (seriously, who in Indonesia is reading my crappy writings willingly? I'm convinced that some countries use me as a torture device.) I just want to thank the readers for giving me the confidence to move forward. If you have any comments you'd like to share, please do. I'd love any criticism, constructive or otherwise. Please let me know what you like, dislike, hope for, are dreading, or any theories you have. PM me if you have character ideas, if you think your OC could fit, I'll try to make it happen. (I need more semi-important character ideas.)

Thank you so much once again!


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